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Hello,
I'd like to search for expression of certain transposable elements that are not in the reference. I added their sequences to the reference fasta, and will see what (if any) aligns to them (usi…
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Hello,
I've run ReLERNN both with and without the --mask option, yet I've obtained identical results (same window size and the resulting table with nSites). For --mask option I provide a .bed file …
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As a beginner in the field of bioinformatics, I am particularly interested in understanding how TEtranscripts performs in the context of long-read sequencing data analysis. Could you please provide in…
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sr320 updated
7 months ago
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Hi sorry to bother you I'm trying to use methylartist for my data, but I am encountering some problems.
First I have my chromosomes named as contig_1, contig_2 ect... in all my data is it a problem…
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Hi there! I have a question about how RiboTricer handles unannotated sequences.
**Purpose**: I am trying to run RiboTricer after generating BAM files using SQUIRE (which does both gene and transpos…
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Dear Shujun,
I hope you are well. When reading your benchmarking paper, “Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline” EDTA appears to …
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Dear @mnshgl0110
Is it normal to identify translocation variants in multiple samples that are in the same reference genome coordinates but translocated to different chromosomes? For example, some …
liu3c updated
3 weeks ago
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Thanks for scTE!
I got a strange output like this when running with self-made index, showing a series of numbers before correct gene/TE names.
![image](https://github.com/JiekaiLab/scTE/assets/967…